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. Author manuscript; available in PMC: 2014 Feb 26.
Published in final edited form as: Proteins. 2012 Feb 10;80(5):1283–1298. doi: 10.1002/prot.24025

Figure 3.

Figure 3

a) Representative snapshot of position 6 C:C (G6C) mismatch and amino acid residues within 4 Å, from non-TI MD simulation. Note proximity of several amino acid residues with this base pair, which explains the sensitivity of binding affinity to a mismatch in this position.

b) Comparison of base pair geometries in position 4 of guide strand in TtAgo 3F73 ternary complex. T:U (A4T) in tan, C:U (A4C) in purple, fully-matched (A:U) colored by element. Representative snapshots are shown for the mismatches; for the fully-matched base pair the 3F73 crystal structure is shown. Note displacements of both guide and target bases in mismatches relative to fully-matched base pair.